I am working through the tutorial, Reduce Sum: A Minimal Example (mc-stan.org). I am able to get the tutorial to work using using Docker with cmdstanr_0.5.1.9000 and Stan 2.29.
I am in the process of converting my own hierarchical occupancy model to run reduce_sum. Conceptually, I loop over units (e.g., sites or visits) and I am trying to use reduce_sum over each unit.
When I use this function without reduce_sum(), the model works for units 1 to n_obs_psi. (This is the index where I am trying to use reduce sums).
target += unit_prob_loop(
any_samples, 1, n_obs_psi, y, k_samples, any_seen,
log_psi, log1m_psi, logit_p, start_idx, end_idx);
However, when I try to use this function with reduce_sum():
target +=
reduce_sum(unit_prob_loop, any_samples, grainsize,
y, k_samples, any_seen,
log_psi, log1m_psi, logit_p, start_idx, end_idx);
Following the example, I though I just needed to place the start and end variables as the 2nd and 3rd inputs and then drop them. The model compiles, but I get an error when I try to use the model:
Running MCMC with 2 parallel chains, with 4 thread(s) per chain...
Chain 1 Unrecoverable error evaluating the log probability at the initial value.
Chain 1 Exception: Exception: array[uni, ...] index: accessing element out of range. index 201 out of range; expecting index to be between 1 and 1 (in '/home/rstudio/Documents/.//occupancy_function.stan', line 74, column 4, included from
Chain 1 Exception: Exception: array[uni, ...] index: accessing element out of range. index 201 out of range; expecting index to be between 1 and 1 (in '/home/rstudio/Documents/.//occupancy_function.stan', line 74, column 4, included from
Chain 1 '/tmp/RtmpRcZsmT/model-4463abae0c1.stan', line 3, column 0) (in '/tmp/RtmpRcZsmT/model-4463abae0c1.stan', line 155, column 2 to line 158, column 56)
Chain 1 Exception: Exception: array[uni, ...] index: accessing element out of range. index 201 out of range; expecting index to be between 1 and 1 (in '/home/rstudio/Documents/.//occupancy_function.stan', line 74, column 4, included from
Chain 1 '/tmp/RtmpRcZsmT/model-4463abae0c1.stan', line 3, column 0) (in '/tmp/RtmpRcZsmT/model-4463abae0c1.stan', line 155, column 2 to line 158, column 56)
Chain 2 Unrecoverable error evaluating the log probability at the initial value.
Chain 2 Exception: Exception: array[uni, ...] index: accessing element out of range. index 101 out of range; expecting index to be between 1 and 1 (in '/home/rstudio/Documents/.//occupancy_function.stan', line 74, column 4, included from
Chain 2 Exception: Exception: array[uni, ...] index: accessing element out of range. index 101 out of range; expecting index to be between 1 and 1 (in '/home/rstudio/Documents/.//occupancy_function.stan', line 74, column 4, included from
Chain 2 '/tmp/RtmpRcZsmT/model-4463abae0c1.stan', line 3, column 0) (in '/tmp/RtmpRcZsmT/model-4463abae0c1.stan', line 155, column 2 to line 158, column 56)
Chain 2 Exception: Exception: array[uni, ...] index: accessing element out of range. index 101 out of range; expecting index to be between 1 and 1 (in '/home/rstudio/Documents/.//occupancy_function.stan', line 74, column 4, included from
Chain 2 '/tmp/RtmpRcZsmT/model-4463abae0c1.stan', line 3, column 0) (in '/tmp/RtmpRcZsmT/model-4463abae0c1.stan', line 155, column 2 to line 158, column 56)
Warning: Chain 1 finished unexpectedly!
Warning: Chain 2 finished unexpectedly!
Warning: Use read_cmdstan_csv() to read the results of the failed chains.
Warning messages:
1: All chains finished unexpectedly! Use the $output(chain_id) method for more information.
2: No chains finished successfully. Unable to retrieve the fit.
>
I am already using the Onion method for the model and this example motivated me to encapsulate code into function. I have attached code for a reproducible example:
-
occupancy_function.stan (1.8 KB) that contains occpuancy model funtions
scale_cholesky_factor.stan (724 Bytes) that contains code used for the onion method
sim_multi.R (2.6 KB) that simulates data and fits the model
occupancy_hm.stan (5.3 KB) that contains the Stan code I am asking about.
Session info:
> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.3 LTS
Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=C
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base
other attached packages:
[1] ggpubr_0.4.0 ggthemes_4.2.4 GGally_2.1.2
[4] forcats_0.5.1 stringr_1.4.0 dplyr_1.0.8
[7] purrr_0.3.4 readr_2.1.2 tidyr_1.2.0
[10] tibble_3.1.6 ggplot2_3.3.5 tidyverse_1.3.1
[13] cmdstanr_0.5.1.9000
loaded via a namespace (and not attached):
[1] nlme_3.1-157 matrixStats_0.61.0
[3] fs_1.5.2 lubridate_1.8.0
[5] RColorBrewer_1.1-3 httr_1.4.2
[7] rstan_2.29.2.9000 tensorA_0.36.2
[9] tools_4.1.2 backports_1.4.1
[11] utf8_1.2.2 R6_2.5.1
[13] DBI_1.1.2 colorspace_2.0-3
[15] withr_2.5.0 tidyselect_1.1.2
[17] gridExtra_2.3 prettyunits_1.1.1
[19] processx_3.5.3 curl_4.3.2
[21] compiler_4.1.2 cli_3.2.0
[23] rvest_1.0.2 xml2_1.3.3
[25] posterior_1.2.1 scales_1.1.1
[27] checkmate_2.0.0 callr_3.7.0
[29] StanHeaders_2.29.2.9000 minqa_1.2.4
[31] pkgconfig_2.0.3 lme4_1.1-29
[33] dbplyr_2.1.1 rlang_1.0.2
[35] readxl_1.4.0 rstudioapi_0.13
[37] farver_2.1.0 generics_0.1.2
[39] jsonlite_1.8.0 car_3.0-12
[41] distributional_0.3.0 inline_0.3.19
[43] magrittr_2.0.3 loo_2.5.1
[45] Matrix_1.4-1 Rcpp_1.0.8.3
[47] munsell_0.5.0 fansi_1.0.3
[49] abind_1.4-5 lifecycle_1.0.1
[51] stringi_1.7.6 carData_3.0-5
[53] MASS_7.3-56 pkgbuild_1.3.1
[55] plyr_1.8.7 grid_4.1.2
[57] parallel_4.1.2 crayon_1.5.1
[59] lattice_0.20-45 haven_2.4.3
[61] splines_4.1.2 hms_1.1.1
[63] knitr_1.38 ps_1.6.0
[65] pillar_1.7.0 boot_1.3-28
[67] ggsignif_0.6.3 codetools_0.2-18
[69] stats4_4.1.2 reprex_2.0.1
[71] glue_1.6.2 V8_4.1.0
[73] data.table_1.14.2 RcppParallel_5.1.5
[75] modelr_0.1.8 nloptr_2.0.0
[77] vctrs_0.4.0 tzdb_0.3.0
[79] cellranger_1.1.0 gtable_0.3.0
[81] reshape_0.8.8 assertthat_0.2.1
[83] xfun_0.30 broom_0.7.12
[85] rstatix_0.7.0 ellipsis_0.3.2